The CSIRO has had its funding slashed and 420 full-time staff will lose their jobs. Photograph: Alan Porritt/AAP

Savage budget cuts will make it harder for science to develop products and processes for the market and will hamper Australia’s transition to a “smart economy”, according to the research industry.

The Co-operative Research Centre (CRC) program, which links researchers with businesses, had its funding cut by $80m, while industry programs such as Commercialisation Australia and enterprise programs designed to cash in on science were abolished.

The chairwoman of the Antarctic CRC, Katherine Woodthorpe, a former chief executive of the Australian Private Equity and Venture Capital Association, said it was “foolish” to take money from other research areas to create a $20bn medical research fund.

“Australia punches above its weight in terms of the proportion of research and development dollars we spend on medical research,” Woodthorpe told the ABC.

“We have some fine [medical] research establishments but we also have some fine research in so many other areas and we are having money taken from them in order to pay for this medical research uplift, and I think that is foolish.”

The CRC Association chief executive, Tony Peacock, said the cut took the program back to its 1996 level in funding, when the Howard government came to office. He said CRC funding had already been cut significantly under Labor and he and the CRC chairman, the former Liberal party director Tony Staley, were surprised by the decision.

“We have done our heavy lifting, we were really surprised at the cuts,” Peacock said.

“It’s not really about the amount of money as much as how you spend it and the stability of long term funding. There is an awful lot of boring research that is required. We need certainty.”

Source: CRC Association

The immediate effect of the funding cut is the end of the latest CRC funding round, which the industry minister, Ian Macfarlane, announced in February.

At the time Macfarlane said: “CRCs bring together key industry partners, world class researchers, the community and government to create new opportunities and develop solutions to assist Australian industries.”

“The benefits of collaboration are well known … CRCs provide amazing opportunities.”

As a result of the funding round ending, industry proposals for research centres, which have often already taken millions of dollars to get to the application stage, may stop completely.

There were between 25 and 30 applications for the round, including a proposed research centre to mitigate food wastage and improve food exports and a proposal for a world-leading research centre on complex project management.

"Eighty million dollars is a lot,” Peacock said. “I feel terrible for those people who have been working so hard on the current funding round.”

While none of the existing 36 CRCs would be affected, there are fears that when their contracts finish, the whole program will be axed.

Research from CRCs has developed products such as the soft contact lens and further development of the cochlear implant. Current CRCs cover areas such as mining, dairy, mental health, autism, low carbon, rail technology, cancer and bushfires.

Woodthorpe said start-up companies trying to capitalise on good science found the Australian market “horrendous” and programs such as Commercialisation Australia were there to help.

“We need these [start-up] companies to provide our economy when we can’t keep digging up the rest of Australia or we can’t keep tourists coming at the numbers they are coming at the moment.

“We need a future economy that is a smart economy. Commercialisation Australia was one of the things that supported that.”

Students from the University of Sydney heckled foreign minister Julie Bishop when she visited the campus on Friday. They were protesting the changes to university fees outlined in the 2014 budget, which could see significantly higher fees under a deregulated system as well as higher interest rates on student loans